Biology subjects

Souza, G.

Publications and source records attributed to Souza, G..

7 recordsLinked to original sources

bioRxiv2026

Ayahuasca plant genomes reveal retrotransposon-derived centromeres and contrasting routes to DMT and β-carbolines

Ayahuasca, used religiously for centuries by Amazonian Indigenous peoples and increasingly studied for its therapeutic potential, owes its psychoactivity to two plants: Psychotria viridis supplies N,N-dimethyltryptamine (DMT), whereas Banisteriopsis caapi supplies beta-carbolines that render DMT orally active. Here we show that the two plants have distinct genome histories: P. viridis is hexaploid (2n = 6x = 66), consistent with autopolyploidy, and B. caapi is diploid (2n = 2x = 20). CENH3-bound regions of both species are nonetheless enriched in CRM-type Ty3/Gypsy retrotransposons, with additional LINE elements and CRM-derived satellites in B. caapi. In P. viridis, a single multifunctional methyltransferase catalyzes both N-methylations of tryptamine to DMT. In B. caapi, beta-carboline biosynthesis combines dedicated enzymes with an acetaldehyde-dependent Pictet-Spengler cyclization that can proceed non-enzymatically, followed by enantioselective oxidation to harmaline. These resources link the ethnobotanical history of ayahuasca to its molecular basis, providing genomes of both source plants, the genetic structure of traditionally recognized cultivated varieties, and the enzymes behind the alkaloids long combined in this decoction.

genomics↗

bioRxiv2025

How much can reticulate evolution entangle plant systematics? Revisiting subfamilial classification of the Malvatheca clade (Malvaceae) on the basis of phylogenomics

Reticulate evolution (RE), involving hybridization and related processes, generates network-like rather than strictly bifurcating relationships among lineages and can obscure phylogenetic relationships. Detecting ancient hybridization is particularly challenging, as genomic signals may erode over time. The Malvatheca clade (Malvaceae), marked by multiple paleopolyploidy events since its estimated origin 66 my, offers a useful model for examining RE. Its three subfamilies--Bombacoideae (with high chromosome numbers, mostly trees), Malvoideae (lower chromosome numbers, mostly herbs), and the recently described Matisioideae--show unresolved relationships, with several taxa of uncertain placement. We conducted a phylogenomic analysis of 62 Malvatheca species via complete plastomes, 35S rDNA cistrons, and comparative repeatome data. All datasets consistently resolved three main clades: (i) Bombacoideae, (ii) Malvoideae, and (iii) a heterogeneous assemblage including most of the recently assigned Matisioideae and several incertae sedis taxa, suggesting a more complex evolutionary history and circumscription than previously recognized. Chromosome numbers were negatively correlated with repeatome diversity: Bombacoideae presented higher counts but lower repeat diversity, possibly reflecting slower repeat evolution associated with woody growth forms. In contrast, clade III showed marked heterogeneity in both chromosome number and repeat composition, which is consistent with a reticulate origin. Overall, our results show evidence of ancient hybridization and polyploidy, predominantly allopolyploidy, in shaping Malvatheca evolution. These results highlight that reticulation and genome dynamics, rather than taxonomic boundaries alone, are central to understanding the diversification of Malvatheca.

genomics↗

bioRxiv2025

Exposure time to moderately high temperature affects photosynthetic response to water deficit in Eucalyptus globulus Labill.

The co-occurrence of drought and heat stress in the field is especially frequent and the plant response to a combination of these abiotic stresses is singular, remaining largely unknown. Understanding physiological responses to a combined stress is of particular importance in face of the imminent global climate changes, which is predicted to entail not only higher temperatures, but also increase in drought, imposing restrictions to the productivity of economically important species as E. globulus. This forest species is critically affected by changes in temperature and water availability, since its high productivity implies in high rates of water use. In order to evaluate the photosynthetic responses of Eucalyptus globulus to these environmental conditions, young plants were grown at 25{degrees} C and 35{degrees} C under different irrigation regimes: full irrigation - FI, moderate drought - MD, and severe drought - SD. Plants grown at 25{degrees} C FI and MD were also subjected to a short-term exposure to 35{degrees} C. Several ecophysiological variables, derived mainly from leaf gas exchange and chlorophyll a fluorescence measurements, were compared in order to test the hypotheses that: i) E. globulus show different responses to short or long-term exposure to 35{degrees} C; ii) the effect of both stresses combined will not be simply the sum of each condition applied separately. Our results showed that plants respond differently to water deficit according to the thermal regime. The combination of water deficit and a long-term exposure to 35{degrees} C caused a down-acclimation of the photosynthetic capacity, while plants under the short-term treatment showed a higher performance, even when compared to the 25{degrees} C control condition, supporting the hypothesis i. Thus, the short-term exposure to 35{degrees} C induced an increase in tolerance to water deficit. Since the response to a combination of heat and drought differed from the superposition of individual responses, as observed mainly at 35{degrees} C, the hypothesis ii was also supported by our results.

plant biology↗

bioRxiv2024

Repeat-based holocentromeres of the woodrush Luzula sylvatica reveal new insights into the evolutionary transition from mono- to holocentricity

Although the centromere is restricted to a single region of the chromosome in most studied eukaryotes, members of the rush family (Juncaceae) harbor either monocentric (Juncus) or holocentric (Luzula) chromosomes. This provides an opportunity to study the evolutionary mechanisms involved in the transition to holocentricity. Here by combining chromosome-scale genome assembly, epigenetic analyses, immuno-FISH, and super-resolution microscopy, we report the occurrence of repeat-based holocentromeres in L. sylvatica. We found an irregular distribution of genes, centromeric units, and most repeats along the chromosomes. We determined the centromere function predominantly associated with two satellite DNA repeats, Lusy1 and Lusy2 of 124- and 174-bp monomer length, respectively, while CENH3 also binds satellite-free gene-poor regions. Comparative repeat analysis revealed that Lusy1 is present in most Luzula species, suggesting a conserved centromere role of this repeat. Synteny between L. sylvatica (n = 6) and J. effusus (n = 21) genomes further evidenced a chromosome number reduction in Luzula derived from multiple chromosome fusions of ancestral J. effusus-like chromosomes. We propose that the transition to holocentricity in Luzula involves: (i) fusion of small chromosomes resembling Juncus-like centromeres; (ii) expansion of atypical centromeric units; and (iii) colonization of satellite DNA for centromere stabilization.

genomics↗

bioRxiv2023

Oligo-barcodes illuminate holocentric karyotype evolution in Rhynchospora (Cyperaceae)

Holocentric karyotypes are assumed to rapidly evolve through chromosome fusions and fissions due to the diffuse nature of their centromeres. Here, we took advantage of the recent availability of a chromosome-scale reference genome for Rhynchospora breviuscula, a model species of this holocentric genus, and developed the first set of oligo-based barcode probes for a holocentric plant. These probes were applied to 13 additional species of the genus, aiming to investigate the evolutionary dynamics driving the karyotype evolution in Rhynchospora. The two sets of probes were composed of 27,392 (green) and 23,968 (magenta) oligonucleotides, and generated 15 distinct FISH signals as a unique barcode pattern for the identification of all five chromosome pairs of the R. breviuscula karyotype. Oligo-FISH comparative analyzes revealed different types of rearrangements, such as fusions, fissions, putative inversions and translocations, as well as genomic duplications among the analyzed species. Two rounds of whole genome duplication (WGD) were demonstrated in R. pubera, but both analyzed accessions differed in the complex chain of events that gave rise to its large, structurally diploidized karyotypes with 2n = 10 or 12. Considering the phylogenetic relationships and divergence time of the species, the specificity and synteny of the probes were maintained up to species with a divergence time of [~]25 My. However, karyotype divergence in more distant species hindered chromosome mapping and the inference of specific events. This barcoding system is a powerful tool to study chromosomal variations and genomic evolution in holocentric chromosomes of Rhynchospora species.

genomics↗

bioRxiv2020

Aiming off the target: studying repetitive DNA using target capture sequencing reads

O_LIWith the advance of high-throughput sequencing (HTS), reduced-representation methods such as target capture sequencing (TCS) emerged as cost-efficient ways of gathering genomic information. As the off-target reads from such sequencing are expected to be similar to genome skims (GS), we assessed the quality of repeat characterization using this data. C_LIO_LIFor this, repeat composition from TCS datasets of five Rhynchospora (Cyperaceae) species were compared with GS data from the same taxa. C_LIO_LIAll the major repetitive DNA families were identified in TCS, including repeats that showed abundances as low as 0.01% in the GS data. Rank correlation between GS and TCS repeat abundances were moderately high (r = 0.58-0.85), increasing after filtering out the targeted loci from the raw TCS reads (r = 0.66-0.92). Repeat data obtained by TCS was also reliable to develop a cytogenetic probe and solve phylogenetic relationships of Rhynchospora species with high support. C_LIO_LIIn light of our results, TCS data can be effectively used for cyto- and phylogenomic investigations of repetitive DNA. Given the growing availability of HTS reads, driven by global phylogenomic projects, our strategy represents a way to recycle genomic data and contribute to a better characterization of plant biodiversity. C_LI

genomics↗

bioRxiv2018

Stressed mothers, tolerant daughters: a case study about the physiological responses and growth of sugarcane plants under water deficit

Drought stress can imprint marks in plants after a previous exposure, leading to a permissive state that facilitates a more effective response to subsequent stress events. Such stress imprints would benefit plants obtained from progenitors previously exposed to drought. Herein, our hypothesis was that daughter plants obtained from mother plants previously exposed to water deficit will perform better under water deficit as compared to those obtained from mothers that did not face stressful conditions. Sugarcane mother plants were grown under well-hydrated conditions or subjected to three cycles of water deficit by water withholding. Then, daughter plants produced through vegetative propagation were subjected to water deficit. Leaf gas exchange was reduced under water deficit and daughters from mothers that experienced water deficit presented a faster recovery of CO2 assimilation and higher instantaneous carboxylation efficiency after rehydration as compared to daughters from mothers that did not face water deficit. Plants obtained from mother plants that faced water deficit showed the highest leaf proline concentration under water deficit as well as higher leaf H2O 2 concentration and leaf ascorbate peroxidase activity regardless of water regime. Under well-watered conditions, daughters from mothers that faced stressful conditions presented higher root H2O2 concentration and root catalase activity than ones from mothers that did not experience water shortage. Such physiological changes were associated with improvements in leaf area and shoot and root dry matter accumulation in daughters from stressed mothers. Our results suggest that root H2O2 concentration is a chemical signal associated with stress memory and improved sugarcane growth. Such findings bring a new perspective to sugarcane production systems, in which stress memory can be explored for improving drought tolerance in rainfed areas.

plant biology↗